7FEH | pdb_00007feh

Crystal structure of human DDR1 in complex with CH5541127

• PDB DOI: https://doi.org/10.2210/pdb7FEH/pdb

• Classification: TRANSFERASE
• Organism(s): Homo sapiens
• Expression System: Spodoptera frugiperda
• Mutation(s): No 


• Deposited: 2021-07-20 Released: 2022-07-27 
• Deposition Author(s): Fukami, T.A., Kadono, S., Matsuura, T.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.61 Å
• R-Value Free: 
  0.206 (Depositor), 0.200 (DCC) 
• R-Value Work: 
  0.166 (Depositor), 0.160 (DCC) 
• R-Value Observed: 
  0.168 (Depositor) 

Literature

Novel potent and highly selective DDR1 inhibitors from integrated lead finding

Kuhn, B., Ritter, M., Benz, J., Kocer, B., Sarie, J.C., Hochstrasser, R., Rudolph, M.G., Kadono, S., Matsuura, T., Murata, T., Richter, H., Prunotto, M.

(2023) Medicinal Chemistry Research 32: 1400-1425

• DOI: https://doi.org/10.1007/s00044-023-03066-2

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 36.84 kDa 
• Atom Count: 2,609 
• Modeled Residue Count: 293 
• Deposited Residue Count: 320 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Epithelial discoidin domain-containing receptor 1	A	320	Homo sapiens	Mutation(s): 0  Gene Names: DDR1 EC: 2.7.10.1
UniProt & NIH Common Fund Data Resources
Find proteins for Q08345 (Homo sapiens) Explore Q08345  Go to UniProtKB:  Q08345
PHAROS:  Q08345 GTEx:  ENSG00000204580

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
3UI (Subject of Investigation/LOI)	B [auth A]	N-[(5-chloranyl-2-ethylsulfonyl-phenyl)methyl]-3-piperazin-1-yl-5-(trifluoromethyloxy)benzamide C21 H23 Cl F3 N3 O4 S FNPFZOPPAGELAN-UHFFFAOYSA-N
NO3	C [auth A], D [auth A]	NITRATE ION N O3 NHNBFGGVMKEFGY-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
3UI	BindingDB:  7FEH	IC50: 84 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.61 Å
• R-Value Free:  0.206 (Depositor), 0.200 (DCC) 
• R-Value Work:  0.166 (Depositor), 0.160 (DCC) 
• R-Value Observed: 0.168 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 40.39	α = 90
b = 61.7	β = 106.22
c = 63.11	γ = 90

Software Package:

Software Name	Purpose
SCALA	data scaling
PHENIX	refinement
PDB_EXTRACT	data extraction
xia2	data reduction
REFMAC	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2022-07-27 
Deposition Author(s): Fukami, T.A., Kadono, S., Matsuura, T.

Revision History  

• Version 1.0: 2022-07-27
  Type: Initial release
  
• Version 1.1: 2023-08-09
  Changes: Database references
• Version 1.2: 2024-05-29
  Changes: Data collection